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Sodium in PDB 4l3h: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide

All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%) 15.4 / 19.8

Other elements in 4l3h:

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide (pdb code 4l3h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide, PDB code: 4l3h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4l3h

Go back to Sodium Binding Sites List in 4l3h
Sodium binding site 1 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:49.7
occ:1.00
 O A:LEU250 2.1 45.2 1.0
O A:HOH681 2.2 56.1 1.0
O A:ILE255 2.4 50.8 1.0
O A:ARG252 2.5 44.2 1.0
O A:HOH607 2.6 49.0 1.0
C A:LEU250 3.3 43.2 1.0
C A:ARG252 3.4 44.0 1.0
C A:ILE255 3.5 46.3 1.0
N A:ILE255 3.9 44.6 1.0
C A:ALA251 3.9 44.2 1.0
OE1 A:GLU256 4.0 59.6 1.0
N A:ARG252 4.0 43.2 1.0
CA A:PRO253 4.1 46.6 1.0
CA A:ILE255 4.1 43.1 1.0
N A:GLY254 4.1 44.7 1.0
N A:PRO253 4.1 46.4 1.0
O A:ALA251 4.1 46.5 1.0
N A:ALA251 4.1 43.0 1.0
CB A:ILE255 4.1 41.6 1.0
CA A:ALA251 4.1 44.1 1.0
CA A:LEU250 4.3 40.5 1.0
CA A:ARG252 4.4 42.3 1.0
OE2 A:GLU256 4.4 64.2 1.0
C A:PRO253 4.4 46.0 1.0
CD A:GLU256 4.4 59.3 1.0
CD1 A:LEU250 4.4 42.6 1.0
N A:GLU256 4.7 46.5 1.0
O A:HOH686 4.7 59.4 1.0
CG A:LEU250 4.7 43.4 1.0
C A:GLY254 4.8 45.7 1.0
O A:LEU249 4.9 39.0 1.0

Sodium binding site 2 out of 4 in 4l3h

Go back to Sodium Binding Sites List in 4l3h
Sodium binding site 2 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:62.3
occ:1.00
 O A:HOH518 2.0 47.4 1.0
OG1 A:THR233 2.5 55.8 1.0
OD1 A:ASN231 2.6 54.6 1.0
O A:HOH680 2.7 48.6 1.0
O A:HOH538 2.8 47.5 1.0
CG A:ASN231 3.5 53.9 1.0
CB A:THR233 3.6 58.6 1.0
ND2 A:ASN231 3.7 50.8 1.0
CG2 A:THR233 3.9 62.0 1.0
N A:THR233 3.9 58.4 1.0
CA A:THR233 4.3 57.5 1.0
N A:ALA234 4.4 55.3 1.0
N A:GLU232 4.8 58.5 1.0
CB A:ASN231 4.8 54.0 1.0
C A:ASN231 4.8 56.8 1.0
C A:THR233 4.9 56.0 1.0

Sodium binding site 3 out of 4 in 4l3h

Go back to Sodium Binding Sites List in 4l3h
Sodium binding site 3 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:33.8
occ:1.00
 O B:HOH824 2.2 39.2 1.0
O B:HOH816 2.3 35.6 1.0
OD1 B:ASN231 2.3 29.0 1.0
OG1 B:THR233 2.4 32.6 1.0
O B:HOH630 2.5 31.2 1.0
O B:HOH731 2.6 35.0 1.0
CG B:ASN231 3.1 30.9 1.0
ND2 B:ASN231 3.4 31.4 1.0
CB B:THR233 3.6 34.2 1.0
O B:HOH652 3.8 41.8 1.0
N B:THR233 3.9 29.2 1.0
CG2 B:THR233 4.0 35.0 1.0
O B:HOH700 4.0 42.0 1.0
CA B:THR233 4.2 31.5 1.0
O B:HOH724 4.3 47.7 1.0
N B:ALA234 4.3 31.4 1.0
O B:HOH803 4.5 46.4 1.0
CB B:ASN231 4.5 27.8 1.0
O B:HOH647 4.5 36.8 1.0
N B:GLU232 4.7 28.4 1.0
C B:ASN231 4.7 28.9 1.0
O B:HOH807 4.8 53.8 1.0
C B:THR233 4.8 31.9 1.0
CA B:ASN231 4.8 29.0 1.0
O B:HOH711 4.8 35.6 1.0

Sodium binding site 4 out of 4 in 4l3h

Go back to Sodium Binding Sites List in 4l3h
Sodium binding site 4 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:34.2
occ:1.00
 O B:LEU250 2.2 32.3 1.0
O B:ILE255 2.2 32.4 1.0
O B:HOH831 2.4 47.3 1.0
O B:HOH661 2.4 39.1 1.0
O B:ARG252 2.6 31.7 1.0
O B:HOH637 2.6 41.7 1.0
C B:LEU250 3.3 29.6 1.0
C B:ILE255 3.4 37.5 1.0
C B:ARG252 3.5 33.1 1.0
N B:ILE255 3.8 34.7 1.0
C B:ALA251 3.8 30.5 1.0
N B:ARG252 3.9 26.5 1.0
CA B:ILE255 4.0 35.1 1.0
CA B:ALA251 4.1 29.8 1.0
O B:ALA251 4.1 30.8 1.0
N B:ALA251 4.1 28.1 1.0
CA B:PRO253 4.2 36.6 1.0
N B:GLY254 4.2 35.3 1.0
CB B:ILE255 4.2 33.8 1.0
N B:PRO253 4.3 37.7 1.0
OE2 B:GLU256 4.3 58.4 1.0
CA B:LEU250 4.3 29.1 1.0
O B:HOH723 4.4 52.1 1.0
CA B:ARG252 4.4 27.3 1.0
CD1 B:LEU250 4.4 34.0 1.0
C B:PRO253 4.5 36.2 1.0
N B:GLU256 4.5 36.0 1.0
CD B:GLU256 4.7 51.5 1.0
CG B:LEU250 4.7 30.1 1.0
OE1 B:GLU256 4.8 56.8 1.0
C B:GLY254 4.8 37.4 1.0
O B:LEU249 4.9 29.1 1.0
CA B:GLU256 4.9 38.4 1.0

Reference:

N.Abu Tarboush, E.T.Yukl, S.Shin, M.Feng, C.M.Wilmot, V.L.Davidson. Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S
Page generated: Mon Oct 7 16:41:26 2024

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